For the first time a transient transfection system was developed for Giardia lamblia using flanking regions of the glutamate dehydrogenase gene and the luciferase reporter gene. This will enable study of transcription of genes such as those that are induced during encystment, genes which undergo antigenic variation and constitutively expressed genes. Cwp2, a second protein constituent of the Giardia lamblia cyst wall was identified and sequenced. Monoclonal antibodies were made to encystment vesicles and cyst walls and were used to identify proteins important in vesicular transport and constituents of the cyst wall. Entamoeba histolytica contains genes encoding proteins normally associated with the mitochondrion, an organelle this organism appears to lack. Sequence and phylogenetic analysis of two such Entamoeba genes has been performed and confirms the specific relatedness. This has major implications for our understanding of the unique biochemistry of this parasite. The same genes have been sought in other parasites thought to lack mitochondria. Analysis of a homologous gene isolated from Trichomonas indicates a similar evolutionary history and implies descent from a mitochondrion bearing ancestor.